| agf | Angiosperms Gymnosperms Ferns |
| AngGym | Angiosperms Gymnosperms |
| A_selected | Adjacency Matrix for Orthology Graph |
| coltips | Colouring Tree Tips |
| gapless_msa | Remove Gaps in a MSA |
| getseqGS | Get the GS Sequence |
| madRoot | Find The Root of a Phylogenetic Tree Using MAD Method |
| mapTrees | Map Gene Tree into Species Tree |
| mltree | Build Up a ML Tree |
| msa | Multiple Sequence Alignment |
| orthG | Infer GS OrthoGroups Within a Set of Species |
| orthP | Search Orthologous of a Given Protein |
| sdf | Seed Plants and Ferns GS |
| selected_tr | Ultrametric Rooted Seed Plants Tree |
| speciesGS | Map Species Names |
| subsetGS | GS Proteins Report |